RE: solvateOct

From: Kristina Furse <>
Date: Sun 1 Dec 2002 15:57:13 -0600

For the sake of completeness (and at the risk of sounding completely
obsessive) I stumbled across one more little detail you may have to watch if
you want to switch water models with a truncated octahedral box. Though the
box dimensions aren't read from the prmtop file anymore, I believe the box
type still may be (set by the IFBOX parameter in the first section of prmtop
%FLAG POINTERS). When I started sander runs with the prmtop made using the
setBox command for the second pass through Leap, I noticed in the mdout file
that the box type was listed as rectilinear. That's when I found IFBOX. When I
manually changed IFBOX to "2" in the prmtop, the box type was reset to
truncated octrahedron (IFBOX = 1 was rectilinear).

Is this flag just a formality? Things did seem to run OK with truncated
octrahedron box dimensions (angle not eq 90) in coordat and IFBOX set to 1.



>===== Original Message From =====
>On Tue, Nov 26, 2002, Kristina Furse wrote:
>> If anyone else tries to do this, I thought I'd mention for the record, I
>> ended up going with the first, more general protocol (details below)--two
>> passes through LEaP, then copied the box information from the first prmtop
>> file to the second (%FLAG BOX_DIMENSIONS section), and then used this
>> modified prmtop with the first coordat (since both were 3pt water models
>> the first one had the correct box info) for the calculation.
>This sounds correct. Amber 7 ignores the BOX_DIMENSIONS in the prmtop (it's
>just there for backwards compatibility), but it doesn't hurt.
>> I initially tried the second, simpler way, but couldn't get it to work. I
>> even used an edited leaprc.ff99 where I went in and replaced any mention of
>> T3P with SPC. From this I would get SPC for the crystallographic water I
>> included, but still got T3P for the additional box water. I took a look at
>> solvents.lib, and please correct me if I'm interpreting it wrong, but I
>> think WATBOX216 may be specific to TIP3P after all. The entry for WATBOX216
>> in solvents.lib seems to have the TIP3P charges included in the
>> "!entry.SPC.unit.atoms table str name str type int typex int resx int
>> flags int seq int elmnt dbl chg" section,
> are correct, and my earlier suggestion was wrong. As you
>note, WATBOX216 has the TIP3P charges, and hence *cannot* be used for
>SPC/E water. Thanks for catching this. (And, of course, WATBOX216 is an
>archaic name, back to the days when the only water model really supported
>by amber was TIP3P. We'll probably have to make WATBOX216 go away in the
>release, to be replaced with a better name.)
>[And, a good object lesson for everyone: just because my initials are the
>bottom of an e-mail doesn't make the information correct. Please follow
>Kristina's example and check things for yourself!]
>Thanks again for the information....regards....dac
>David A. Case | e-mail:
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA |

Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Received on Sun Dec 01 2002 - 13:57:13 PST
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